Up to now MSH2/MLH1 and APC gene mutations have been considered as the major cause of inherited colorectal cancer (CRC). Carriers of mutations within the above genes have a very high risk of cancer, but they constitute only a few percent only of all CRC.
It has been reported that having a chronic inflammatory status longer than 8-10 years is also related to an increased risk of CRC. Despite long-term efforts aimed to find the way of diagnosing the predisposition to CRC, a procedure allowing this has not yet been discovered.
NOD2 gene has been mapped on chromosome 16q12 (Ogura et al., J. Biol. Chem. 2001; 276: 4812-4818). It contains 12 exons and encodes a protein composed of 1040 of amino acids. In 2001, a correlation between 3020insC in exon 11 of NOD2 and the occurrence of Crohn's disease (CD) was shown. PCT Publication WO 02/44426 presents the sequence of NOD2 as well as the relation between distinct variants of this gene (including a variant with 3020insC) and CD. CD and ulcerative colitis are recognized as inflammatory bowel diseases.
CHEK2, (also known as CHK2 [MIM 604373]) is located on chromosome 22q and encodes the human analogue of yeast Cds1 and Rad53, which are checkpoint kinases. Activation of these proteins in response to DNA damage prevents cellular entry into mitosis. CHEK2 is activated through phosphorylation by ATM in response to DNA damage induced by ionizing radiation. Activated CHEK2 phosphorylates BRCA1 and TP53 proteins, regulating tumor suppressor function of these proteins (Matsuoka et al., Proc. Natl. Acad. Sci. USA, 97: 10389-10394, 2000, Chaturvedi et al., Oncogene, 18: 4047-54, 1999, Ahn et al., Cancer Res., 60: 5934-6, 2000, Falck et al., Nature, 410: 842-847, 2001, Chehab et al., Genes Dev., 14: 278-288, 2000, Shieh et al., Genes Dev., 14: 289-300, 2000, Lee et al., Nature, 404: 201-204, 2000.).
In Poland there are three polymorphic variants of CHEK2, which in aggregate are present in 5.7% of the population; two of these (1100delC and IVS2+1G>A) are rare and result in premature protein truncation. The third is a common missense variant (I157T) that results in the substitution of an isoleucine for a threonine. All three variants have been found to be associated with a predisposition to prostate cancer. The CHEK2 protein is expressed in a wide range of tissues and the full range of cancers associated with inactivating CHEK2 mutations has not yet been determined.
The IVS2+1G>A mutation creates a 4-bp insertion due to abnormal splicing, creates premature protein termination codon in exon 3 and leads to the disruption of protein expression. There are no reports suggesting correlation between the CHEK2 IVS2+1G>A allele alone and increased predisposition to cancer. The IVS2+1G>A variant has been reported previously only in a single family with prostate cancer in the United States (Dong et al., Am. J. Hum. Genet., 72: 270-280, 2003). However, the IVS2+1G>A allele did not segregate with prostate cancer within this family and it was not proven that the IVS2+1G>A confer increased prostate cancer risk.
The 1100delC variant of CHEK2 is present with a 1.1-1.4% frequency in normal population in the European countries studied so far but in North America the allele appears to be relatively rare (CHEK2 Breast Cancer Consortium, Nature Genet., 31: 55-59, 2002; Offit et al., BMC Med. Genet. 15: 1, 2003). This allele has been found to confer a modestly elevated risk of breast and prostate cancer.
The most common CHEK2 variant identified so far was Ile157Thr. The role of this variant, however, is controversial, even though both genetic and biochemical data from previous studies suggest that this mutation can be deleterious (Falck et al., Nature, 410: 842-847, 2001, Bell et al., Science 286: 2528-2531, 1999, Li et al., Mol Cell 9: 1045-1054, 2002). On the other hand, this mutation was found in 2.1% (2/95) of healthy population control individuals in Finland and was proposed as a polymorphism (Vahteristo et al., Cancer Res. 61: 5718-5722, 2001). Other reports also indicate that this mutation is relatively common in normal healthy control individuals (CHEK2 Breast Cancer Consortium, Nature Genet., 31: 55-59, 2002, Allinen et al., Am. J. Hum. Genet., 72: 1023-1028, 2003). This allele does not appear to increase the risk of breast and prostate cancers (Allinen et al., Am. J. Hum. Genet., 72: 1023-1028, 2003). On the other hand one report suggests that I157T variant is a low penetrance allele for prostate cancer (Seppala et al., Br. J. Cancer, 89: 1966-1970, 2003). Whether this functionally related CHEK2 variant confers susceptibility to prostate cancer, or even to other cancers, remained to be clarified.
CDKN2A gene (OMIM 60160) is a tumor supressor gene regarded as the major melanoma susceptibility gene. (Hashemi et al., Nature, 366: 704-707, 1993). Its protein product p16 is a cyclin-dependent kinase inhibitor that suppresses cell proliferation (Whelan et al., New Eng. J. Med. 33: 975-977, 1995). CDKN2A variants are associated with strong (it is with high penetrance—responsible for strong cancer familial aggregation) predisposition to melanoma and cancers of breast, pancreas and larynx (Whelan et al., New Eng. J. Med., 33: 975-977, 1995; Borg et al., J. Natl. Cancer Inst., 92: 1260-1266, 2000, Smigiel et al., Mol Carcinog., 39: 147-54, 2004).
In the U.S. Patent Publication U.S. 20030175721, CDKN2A variants associated with increased melanoma predisposition have been described. There is also some evidence to indicate a possible association between CDKN2A and head and neck cancer (Schneider-Stock et al., Am. J. Hum. Genet., 72: 216-218, 2003), respiratory malignancies (Belinsky et al., Proc. Natl. Acad. Sci. USA, 95: 11891-11896, 1998) and colorectal cancer (Burri et al., Lab. Invest., 81: 217-229, 2001).
In Poland common CDKN2A variants have been reported. One of them—an alanine to threonine substitution at codon 148 (A148T)—has been estimated to be present in approximately 3-3.5% of the population (Debniak et al., Int. J. Cancer, 110 :558-562, 2004; Lamperska et al., Acta Biochim. Pol., 49: 369-376, 2002). Functional studies suggest that this variant is a polymorphism which appears to have no major affect on p16 function (Ranade et al., Nature Genet; 10: 114-116, 1995; Lilischkis et al., Int. J. Cancer, 66: 249-254, 1996). Nevertheless, the A148T change has been found to be over-represented in melanoma kindreds (3%) in comparison to the general population (1.8%) (Queensland, Australia) (Aitken et al., J. Natl. Cancer Inst., 9: 446-452, 1999). Preliminary results of our recent population-based study also suggest that A148T change can be associated with increased melanoma risk. A series of around 400 melanoma cases and around 1000 controls (˜500 newborns and ˜500 adults) was examined. The Nt442g>a (A148T) prevalence was 2.5-fold increased among melanoma patients. No overrepresentation of the Nt500c>g and the Nt540c>t polymorphisms in Polish melanoma population was observed. The A148T carrier population (heterozygous G/A alleles) was more likely to have a relative with malignancy compared to the non-carrier population (57% versus 36%, respectively (p=0.03)).
Prostate cancer is a leading cause of morbidity and mortality in men. Outside of the context of a family history, relatively little is known about the genetic determinants that cause prostate cancer. Epidemiological studies suggest that 5-10% of all prostate cancers are attributable to high penetrance susceptibility genes. The strongest evidence for the role of inherited genetic factors in development of prostate cancer comes from a Scandinavian study on twins that suggested that as many as 42% of prostate cancer risk could be explained by an inherited predisposition (Lichtenstein et al., N. Engl. J. Med., 343: 78-85, 2000). Evidence also points at a complex genetic basis of prostate cancer, involving multiple susceptibility genes and variable phenotypic expression. Different chromosomal loci have been linked to prostate cancer including: HPC1, HPC2, PCAP, CAPB, HPCX, 20q13, 16q23. However, no major prostate susceptibility genes have so far been identified. Only two studies have shown any success cloning candidate susceptibility genes from these regions: HPC1 (MIM 601518) and HPC2/ELAC2 (MIM 605367) (Tavtigian et al., Nature Genet., 27: 172-180, 2001; Carpten et al., Nature Genet., 30: 181-184, 2002). However, other studies suggested a limited role for those genes in hereditary prostate canter (Wang et al., Cancer Res., 61: 6494-6499, 2001.; Xu et al., Am. J. Hum. Genet., 68: 901-911, 2001; and Rebbeck et al., Am. J. Hum. Genet., 67: 1014-1019, 2000).
Breast cancer is a common disease. Each year, approximately 200,000 women in the United States alone are diagnosed with breast cancer, and one in nine American women will develop breast cancer in her lifetime. Hereditary breast cancer is caused by a mutated gene passed from parents to their children. Estimates of the incidence of hereditary breast cancer range from between 5 to 10 percent to as many as 27 percent of all breast cancers.
In 1994, the first gene associated with breast cancer, BRCA1 (BReast CAncer1) was identified on chromosome 17. A year later, a second gene associated with breast cancer, BRCA2, was discovered on chromosome 13. When individuals carry a mutated form of either BRCA1 or BRCA2, they have a high risk of developing breast cancer. Not all hereditary breast cancers are caused by BRCA1 and BRCA2. In fact, a large proportion of breast cancers is not associated with mutation of these two genes.
Despite of longstanding research efforts aimed to develop a mode of diagnosing increased predisposition to cancers of various sites, such diagnostic methods are still needed.
Accordingly, there is a need for the identification of genetic markers that indicate a predisposition for developing cancer and/or malignancies of various sites, (e.g., colorectal cancer, malignant melanoma, such tumors as cancers of the prostate, breast, thyroid, stomach, colon, kidney, lung, pancreas and larynx and myeloproliferative syndrome), that can be used to identify subjects that have an increased susceptibility for developing cancer and/or malignancies, i.e., they are predisposed to develop cancer and/or malignancies.